Hi OP, you mention an underwater event, how about overwatering? Are you pH adjusting? New growth you mention is knarly, possible overwatering + pH out of range. Please provide more detail on watering/pH/feeding.
I'd not try a transplant if she's already in your planned final pot size, unless you went bigger. Add medium for sure, you have room to bury her a bit more.
I'd focus on insuring you're feeding/watering/pH adjusting correctly before fimming. You want her healthy for quick recovery. Talk more about LED wall draw or chip wattage for optimal light distance.
Regarding trimming, it's an ongoing process, you want growth tips shooting up, you can determine how many growth tips become colas through pruning. Short answer, you can prune through veg and in to flower. you want buds to be above the veg canopy that forms before flip to flower. You can trim the shit that shoots out under canopy during flower, as they'll make larf buds given inadequate light penetration.